Variant report

Variant	rs4888367
Chromosome Location	chr16:75292120-75292121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75291818-75293396	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:75291830-75292155	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75291813..75293681-chr16:75338481..75340781,2	MCF-7	breast:
2	chr16:75290897..75293709-chr16:75420736..75422960,2	K562	blood:
3	chr16:75291273..75292814-chr16:75345421..75347980,2	MCF-7	breast:
4	chr16:75288586..75292639-chr16:75337750..75340619,6	MCF-7	breast:
5	chr16:75290787..75293360-chr16:75358272..75360844,2	K562	blood:

No data

Variant related genes	Relation type
BCAR1	TF binding region
ENSG00000259999	Chromatin interaction
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11645408	0.80[ASN][1000 genomes]
rs11647214	0.84[ASN][1000 genomes]
rs12932495	0.84[ASN][1000 genomes]
rs1469121	0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs35091778	0.89[ASN][1000 genomes]
rs3784938	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv1056082	chr16:75004990-75295847	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv516504	chr16:75223491-75306402	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv1806781	chr16:75235390-75307470	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv906909	chr16:75236154-75316074	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	esv1792587	chr16:75237936-75305783	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv906910	chr16:75251299-75316074	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv906911	chr16:75252526-75296247	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv906912	chr16:75252526-75320827	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv1813349	chr16:75257361-75302684	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
16	nsv906913	chr16:75267743-75306402	Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
17	nsv471095	chr16:75269533-75320827	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
18	esv1843498	chr16:75271642-75296844	Genic enhancers Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4888367	ADAT1	cis	cerebellum	SCAN
rs4888367	WWP2	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75285600-75292400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr16:75285600-75293000	Enhancers	Lung	lung
3	chr16:75285600-75293000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr16:75285600-75293200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:75285800-75292800	Enhancers	Right Atrium	heart
6	chr16:75286000-75292200	Enhancers	Stomach Mucosa	stomach
7	chr16:75286000-75292200	Enhancers	NHEK	skin
8	chr16:75286000-75292400	Enhancers	Fetal Intestine Large	intestine
9	chr16:75286000-75293000	Enhancers	Left Ventricle	heart
10	chr16:75286000-75293000	Enhancers	Ovary	ovary
11	chr16:75286000-75293200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:75286000-75293200	Enhancers	Fetal Lung	lung
13	chr16:75286000-75293200	Enhancers	NHDF-Ad	bronchial
14	chr16:75286000-75293400	Enhancers	HMEC	breast
15	chr16:75286000-75297400	Enhancers	Psoas Muscle	Psoas
16	chr16:75286000-75297600	Genic enhancers	Fetal Intestine Small	intestine
17	chr16:75286000-75298000	Genic enhancers	Fetal Stomach	stomach
18	chr16:75286200-75292200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:75286200-75293000	Enhancers	Brain Substantia Nigra	brain
20	chr16:75286200-75293200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr16:75286200-75293200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr16:75286200-75293200	Enhancers	Fetal Heart	heart
23	chr16:75286200-75293400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr16:75286400-75293000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr16:75286400-75293200	Enhancers	Brain Anterior Caudate	brain
26	chr16:75286600-75293400	Enhancers	Spleen	Spleen
27	chr16:75287600-75293200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr16:75287800-75292200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr16:75287800-75292600	Enhancers	HSMM	muscle
30	chr16:75287800-75292800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:75287800-75292800	Enhancers	NH-A	brain
32	chr16:75287800-75293000	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr16:75288200-75292200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr16:75288200-75293200	Enhancers	Placenta	Placenta
35	chr16:75288400-75293200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr16:75288800-75292400	Enhancers	Osteobl	bone
37	chr16:75289000-75297400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr16:75289200-75292400	Enhancers	Gastric	stomach
39	chr16:75289200-75293000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:75289200-75298600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr16:75289400-75295000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr16:75289600-75293000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr16:75289800-75292400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr16:75289800-75293000	Enhancers	Liver	Liver
45	chr16:75289800-75293200	Enhancers	Brain Angular Gyrus	brain
46	chr16:75289800-75293200	Enhancers	Brain Hippocampus Middle	brain
47	chr16:75289800-75293200	Enhancers	Colon Smooth Muscle	Colon
48	chr16:75289800-75293400	Enhancers	Pancreas	Pancrea
49	chr16:75290000-75292200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr16:75290000-75292200	Bivalent Enhancer	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links